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comparison print_reads.xml @ 6:35c00763cb5c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
children
comparison
equal deleted inserted replaced
5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_print_reads" name="Print Reads" version="@VERSION@.0"> 1 <tool id="gatk2_print_reads" name="Print Reads" version="@VERSION@.0">
2 <description>on BAM files</description> 2 <description>on BAM files</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
7 <command interpreter="python"> 8 <command interpreter="python">
8 gatk2_wrapper.py 9 gatk2_wrapper.py
9 --stdout "${output_log}" 10 --stdout "${output_log}"
10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" 11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": 12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
18 \$GATK2_SITE_OPTIONS 19 \$GATK2_SITE_OPTIONS
19 20
20 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 21 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
21 --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-6} 22 --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-6}
22 23
23
24 #if $reference_source.reference_source_selector != "history": 24 #if $reference_source.reference_source_selector != "history":
25 -R "${reference_source.ref_file.fields.path}" 25 -R "${reference_source.ref_file.fields.path}"
26 #end if 26 #end if
27 #if str($input_recal) != 'None': 27 #if str($input_recal) != 'None':
28 --BQSR "${input_recal}" 28 --BQSR "${input_recal}"
29 #end if 29 #end if
30 --disable_bam_indexing 30 --disable_bam_indexing
31 ' 31 '
32 32
33 #include source=$standard_gatk_options# 33 #include source=$standard_gatk_options#
34 34
35 ##start analysis specific options 35 ##start analysis specific options
36 #if $analysis_param_type.analysis_param_type_selector == "advanced": 36 #if $analysis_param_type.analysis_param_type_selector == "advanced":
37 -p ' 37 -p '
38 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set": 38 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
39 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}" 39 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
48 --force_platform "${analysis_param_type.force_platform}" 48 --force_platform "${analysis_param_type.force_platform}"
49 #end if 49 #end if
50 ${analysis_param_type.exception_if_no_tile} 50 ${analysis_param_type.exception_if_no_tile}
51 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set": 51 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
52 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default": 52 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
53 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}" 53 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
54 #end if 54 #end if
55 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default": 55 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
56 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}" 56 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
57 #end if 57 #end if
58 #end if 58 #end if
59 ${analysis_param_type.simplify_bam} 59 ${analysis_param_type.simplify_bam}
60 --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}" 60 --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}"
61 --smoothing "${analysis_param_type.smoothing}" 61 --smoothing "${analysis_param_type.smoothing}"
65 ${analysis_param_type.do_not_write_original_quals} 65 ${analysis_param_type.do_not_write_original_quals}
66 ' 66 '
67 #end if 67 #end if
68 </command> 68 </command>
69 <inputs> 69 <inputs>
70 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" 70 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file"
71 help="The input covariates table file which enables on-the-fly base quality score recalibration (intended for use with BaseRecalibrator files) (-BQSR,--BQSR)" /> 71 help="The input covariates table file which enables on-the-fly base quality score recalibration (intended for use with BaseRecalibrator files) (-BQSR,--BQSR)" />
72 <conditional name="reference_source"> 72 <conditional name="reference_source">
73 <expand macro="reference_source_selector_param" /> 73 <expand macro="reference_source_selector_param" />
74 <when value="cached"> 74 <when value="cached">
75 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 75 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
90 <filter type="data_meta" key="dbkey" ref="input_bam" /> 90 <filter type="data_meta" key="dbkey" ref="input_bam" />
91 </options> 91 </options>
92 </param> 92 </param>
93 </when> 93 </when>
94 </conditional> 94 </conditional>
95 95
96 <expand macro="gatk_param_type_conditional" /> 96 <expand macro="gatk_param_type_conditional" />
97 97
98
99 <conditional name="analysis_param_type"> 98 <conditional name="analysis_param_type">
100 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> 99 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
101 <option value="basic" selected="True">Basic</option> 100 <option value="basic" selected="True">Basic</option>
102 <option value="advanced">Advanced</option> 101 <option value="advanced">Advanced</option>
103 </param> 102 </param>
180 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> 179 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
181 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 180 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
182 </outputs> 181 </outputs>
183 <tests> 182 <tests>
184 <test> 183 <test>
185 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 184 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
186 <param name="reference_source_selector" value="history" /> 185 <param name="reference_source_selector" value="history" />
187 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 186 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
188 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /> 187 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
189 <param name="gatk_param_type_selector" value="basic" /> 188 <param name="gatk_param_type_selector" value="basic" />
190 <param name="analysis_param_type_selector" value="basic" /> 189 <param name="analysis_param_type_selector" value="basic" />